The city has suspended boating from public sites on Newtown Creek — a move that potentially wipes out recreation on the polluted waterway as the federal government begins a long clean-up.

A Department of Environmental Protection said its short-term ban on launching boats from city-owned sites would remain in place until the state analyzes the creek’s water quality.

The move comes two months after the federal government listed the 3.5-mile Newtown Creek as a Superfund site — beginning a decade-long hundreds-of-millions-of-dollars clean-up.

Matt Mahoney, an official with the Department of Environmental Protection, said the city was banning recreational use of the waterways out of “an abundance of caution” with regards to public health.

But frustrated community members and environmental advocates castigated the agency for “deliberately crippling” recreation on the creek without having any public health data.

“No kayaker has been hurt or gotten sick after years of use of the public waterways,” said Kathleen Schmid, head of the Newtown Creek Alliance. “The city, as well as the kayakers, have known the state of Newtown Creek’s waters for years and the city felt no compunction to limit access based on information that they have themselves collected.”

The timing of the announcement arrives paradoxically as other city agencies are investing in new ways to expand public access along Newtown Creek — including a renovated park at the end of Manhattan Avenue and a proposed boat launch inside the ground floor of the Greenpoint Manufacturing and Design Center.

The city has already moved to prohibit boating at the Newtown Creek Nature Walk, which it manages, where community members discovered a “No Kayaking” sign at the park’s entrance a month ago, though community members think that the restricted public access is simply about liability in the post-Superfund world.

“We have been aware of pollution for a long time,” said Greenpoint resident Laura Hofmann. “Now that it’s a matter of money, the Department of Environmental Protection suddenly cares.”

The agency will hold a public meeting in December for community members to air their concerns about the policy change. The as-yet-unscheduled meeting should be lively, said Community Board 1 member Dewey Thompson.

“We’re not going to take this lying down,” said Thompson. “This is bulls—t. There’s going to be a very big reaction from the people who use this creek who have stewardship over this if the city goes ahead with this misguided plan to ban even temporarily launching of kayaks and canoes on the waterway.”